I need to know the bootstrap method used by defaul in AMOS. Can somebody help? Thanks ...
Hello, I'm having this issue too.
stopping in step 41
Hi, This is the new log. ESC[0;35m###### Wed Apr 22 05:43:48 BST 2020: Running layoutESC[0m INPUT reads lis mates PLACEMENT CONFLICT ASSEMBLY OUTPUT ESC[0;35m###### Sun Apr 26 17:18:38 BST 2020: Running consensusESC[0m Entering 'Amos_supercontigs.bnk' Found CTG bank unlocking 'r 432968 tk19812' Found FRG bank Found LAY bank Found LIB bank Found RED bank Found SCF bank Found UNV bank IFOs found: 7 File locks: 0 Bank locks: 1 Starting on Sun Apr 26 17:18:38 2020 Read bank is Amos_supercontigs.bnk Alignment...
I'm suspecting it's a memory issue. Is there any chance I can split the delta file to run part of that and reconnect them after? Cheers F
Now I don't have it anymore, but the log file was just listing the different stages of the job like: INPUT reads lis ... till the end without returning any expicit error. F
Yes that is correct it is failing because of the missing CTG files. Is there a amos log file with logging from the casm-layout step? On Sat, Apr 25, 2020 at 12:34 PM Francesco Cicconardi francicco@users.sourceforge.net wrote: Hi, I think consensus fails because layout didn't generate the file. layout also finishes without error messages Thanks a lot F [bugs:#29] https://sourceforge.net/p/amos/bugs/29/ casm-layout ERROR* Status: open Group: v1.x.x Created: Wed Apr 15, 2020 02:37 PM UTC by Francesco...
Hi, I think consensus fails because layout didn't generate the file. layout also finishes without error messages Thanks a lot F
How are you running "concensus" if the casm-layout program had already failed to produce the CTG bank files? What was the error or log from casm-layout? On Wed, Apr 15, 2020 at 10:37 AM Francesco Cicconardi francicco@users.sourceforge.net wrote: Unfortunately casm-layout: casm-layout -t 1000 -U ${supercontigs}.layout -C ${supercontigs}.conflict -b ${supercontigs}.bnk ${supercontigs}.delta fails to generate the some files, specifically CTG.0.map, CTG.0.0.fix and CTG.0.0.var I get the following error...
casm-layout ERROR
I have exactly the same problem...
Hello, Lisa! I have install problem to. May be this help you https://vcru.wisc.edu/simonlab/bioinformatics/programs/install/amos.htm
I am not sure what to do anymore can anyone help me. it looks like i am having problems with utility_AMOS Thanks Attached it the errors.
by using CXXFLAGS="$CXXFLAGS -Wno-narrowing" in configure, it solves the problem. But then, when i press make, it gives these errors: .... make[3]: Entering directory '/home/potant/Downloads/amos-3.1.0/src/Align' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -Wno-narrowing -Wcpp -MT genome-complexity-fast.o -MD -MP -MF .deps/genome-complexity-fast.Tpo -c -o genome-complexity-fast.o genome-complexity-fast.cc...
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS -I../.. -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wno-cpp -c -o libAMOS_a-utility_AMOS.o `test -f 'utility_AMOS.cc' || echo '/apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/'`utility_AMOS.cc In file included from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:10: /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh: In function 'std::__cxx11::string AMOS::Decode(AMOS::NCode_t)': /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:78:25: warning: narrowing conversion of '(ncode & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:78:55: warning: narrowing conversion of '((ncode >> 8) & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:79:35: warning: narrowing conversion of '(((ncode >> 8) >> 8) & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ In file included from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/Message_AMOS.hh:14, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/Universal_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/Link_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/Edge_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/ContigEdge_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/universals_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/universals_AMOS.cc:10: /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh: In function 'std::__cxx11::string AMOS::Decode(AMOS::NCode_t)': /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:78:25: warning: narrowing conversion of '(ncode & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:78:55: warning: narrowing conversion of '((ncode >> 8) & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:79:35: warning: narrowing conversion of '(((ncode >> 8) >> 8) & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc: At global scope: /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '128' from 'int' to 'char' inside { } [-Wnarrowing] }; ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '129' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '130' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '131' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '132' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '133' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '134' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '135' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '136' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '137' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '138' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '139' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '140' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '141' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '142' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '143' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '144' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '145' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '146' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '147' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '148' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '149' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '150' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '151' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '152' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '153' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '154' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '155' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '156' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '157' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '158' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '159' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '160' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '161' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '162' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '163' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '164' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '165' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '166' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '167' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '168' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '169' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '170' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '171' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '172' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '173' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '174' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '175' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '176' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '177' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '178' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '179' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '180' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '181' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '182' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '183' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '184' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '185' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '186' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '187' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '188' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '189' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '190' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '191' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '192' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '193' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '194' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '195' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '196' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '197' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '198' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '199' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '200' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '201' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '202' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '203' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '204' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '205' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '206' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '207' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '208' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '209' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '210' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '211' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '212' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '213' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '214' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '215' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '216' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '217' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '218' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '219' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '220' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '221' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '222' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '223' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '224' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '225' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '226' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '227' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '228' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '229' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '230' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '231' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '232' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '233' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '234' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '235' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '236' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '237' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '238' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '239' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '240' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '241' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '242' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '243' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '244' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '245' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '246' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '247' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '248' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '249' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '250' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '251' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '252' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '253' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '254' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '255' from 'int' to 'char' inside { } [-Wnarrowing] make[3]: *** [Makefile:1059: libAMOS_a-utility_AMOS.o] Error 1
src/Align/genome-complexity-fast.cc:602:26: error: qualified-id in declaration before 'm'
Hi, I am running a amos pipleline that produced the following error: hash-overlap -B -o 35 -x .020 -v 0 ./all.bnk exited with status: 1 What does exited with status: 1 mean?
I am creating a measurement model with 12 latent variables and want to create correlations...
Thanks for the patch, it updated the path vars in minimus2! If anyone could benefit...
Thanks for the patch, it updated the path vars in minimus2! However, there is still...
Thanks for the patch, it updated the path vars in minimus2! However, there is still...
Thanks for the patch, it updated the path vars in minimus2! However, there is still...
Thanks for the patch, it updated the path vars in minimus2! However, there is still...
Thanks for the patch, it worked! If anyone could benefit from the steps: first installed...
Try: https://github.com/nathanhaigh/amos
See: https://github.com/nathanhaigh/amos
Impacts: FreeBSD-9.1 with gcc 4.8 OS X 10.9.5 with gcc 4.9 from MacPorts
add nchart
add find-redundant.pl
Merge branch 'master' of ssh://git.code.sf.net/...
Hello, I am using the following protocol to Merge a multikmer assembly using CDHit...
Hello, I am using the following protocol to Merge a multikmer assembly using CDHit...
Minimus2 stuck at step 20
ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround...
The wiki is back up and running at http://amos.sourceforge.net/wiki/index.php/AMOS...
Home
I am having some trouble running minimus2 on centos 7, I have my .afg file containing...
here is a patch for the DELTAFILTER and SHOWCOORDS variables. It seems that the variables...
ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround...
Where did the detailed wiki of all the features, components and examples of the myriad...
ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround...
Hello everyone, first of all thanks for this great program to the developers and...
Bug fix for segfault while calculating alignments
Merge branch 'master' of ssh://git.code.sf.net/...
More robust fasta parsing in samtoarg.pl
Error in Message parsing code when final qlt field char is '.'